tbuckley/cabot-search huggingface dataset:
Deep-learning algorithm to detect fibrosing interstitial lung disease on chest radiographs
Authors: Hirotaka Nishikiori, Koji Kuronuma, Kenichi Hirota, Naoya Yama, Tomohiro Suzuki, Maki Onodera, Koichi Onodera, Kimiyuki Ikeda, Yuki Mori, Yuichiro Asai, Yuzo Takagi, Seiwa Honda, Hirofumi Ohnishi, Masamitsu Hatakenaka, Hiroki Takahashi, Hirofumi Chiba
Journal: European Respiratory Journal (2022)

Background Antifibrotic therapies are available to treat chronic fibrosing interstitial lung diseases (CF-ILDs), including idiopathic pulmonary fibrosis. Early use of these treatments is recommended to slow deterioration of respiratory function and to prevent acute exacerbation. However, identifying patients in the early stages of CF-ILD using chest radiographs is challenging. In this study, we developed and tested a deep-learning algorithm to detect CF-ILD using chest radiograph images. Method From the image archive of Sapporo Medical University Hospital, 653 chest radiographs from 263 patients with CF-ILDs and 506 from 506 patients without CF-ILD were identified; 921 were used for deep learning and 238 were used for algorithm testing. The algorithm was designed to output a numerical score ranging from 0 to 1, representing the probability of CF-ILD. Using the testing dataset, the algorithm's capability to identify CF-ILD was compared with that of doctors. A second dataset, in which CF-ILD was confirmed using computed tomography images, was used to further evaluate the algorithm's performance. Results The area under the receiver operating characteristic curve, which indicates the algorithm's detection capability, was 0.979. Using a score cut-off of 0.267, the sensitivity and specificity of detection were 0.896 and 1.000, respectively. These data showed that the algorithm's performance was noninferior to that of doctors, including pulmonologists and radiologists; performance was verified using the second dataset. Conclusions We developed a deep-learning algorithm to detect CF-ILDs using chest radiograph images. The algorithm's detection capability was noninferior to that of doctors.
Reply to: Broadening concepts of core pathobiology in various aspects of COPD development
Authors: Feng Xu, Dragos Vasilescu, Wan Tan, Jim Hogg, Tillie-Louise Hackett
Journal: European Respiratory Journal (2022)

We thank E.H. Walters and co-workers for highlighting the innovation of our study [1] using micro-computed tomography (micro-CT) imaging to match tissue pathology with its gene transcriptome, in order to understand the pathobiology of small airway disease in end-stage COPD. We agree with the authors that post-transplant, explanted COPD lungs do represent the end stages of the disease; however, such lung samples provide the only opportunity to assess the entire lung structure and the heterogeneity of small airway disease and emphysema across lung height without the presence of cancer. As the authors note, we have previously shown that destruction of the last generation of small conducting airways, the terminal bronchioles, precedes emphysematous tissue destruction in end-stage COPD [2]. More recently, this work has been validated using formalin-fixed-paraffin embedded (FFPE) samples from patients with mild and moderate COPD, which demonstrated over 41% of their terminal bronchioles are destroyed prior to the detection of emphysema on clinical CT or microscopically on micro-CT [3]. These data highlight that loss of terminal bronchioles occurs early in the disease process and understanding the pathobiology of terminal bronchiole reduction has the potential to develop new therapeutics for COPD. Understanding the pathology of COPD by assessing the "hot spots" or earliest regions of small airway disease <https://bit.ly/3SSql1L>
Reply to: Ventilation and tumour spread: still a pending matter
Authors: Inés López-Alonso, Antonio Fueyo, Guillermo M. Albaiceta
Journal: European Respiratory Journal (2022)

We thank Liu Zhang and co-workers for their interest in our manuscript on the role of mechanical ventilation as an activator of lung tumour cells and promoter of distant metastases [1]. Our study spans from cell cultures to animal models and clinical data to illustrate the impact of mechanical stimulation on cancer cells, trying to put it in a clinical context and pointing to novel therapeutic strategies. Mechanical ventilation in presence of a lung neoplasm highlights the relevance of mechanotransduction in cancer cells and opens novel therapeutic approaches <https://bit.ly/3fu5Jyr>
Blood volatile organic compounds associated with non-reversible and reversible airflow obstruction in US adults
Authors: Angelico Mendy, Ashley L. Merianos, Tesfaye B. Mersha, E. Melinda Mahabee-Gittens
Journal: European Respiratory Journal (2022)

<b>In this study sample representative of the US adult population, blood xylenes, bromodichloromethane and dibromochloromethane are associated with non-reversible airflow obstruction, whereas blood styrene is associated with reversible airflow obstruction</b>https://bit.ly/3ybdyQa
Rhinitis phenotypes and multimorbidities in the general population: the CONSTANCES cohort
Authors: Marine Savouré, Jean Bousquet, Bénédicte Leynaert, Adeline Renuy, Valérie Siroux, Marcel Goldberg, Marie Zins, Bénédicte Jacquemin, Rachel Nadif
Journal: European Respiratory Journal (2022)

Background Scarce epidemiological studies have characterised allergic rhinitis (AR) and non-allergic rhinitis (NAR) in adults. In a population-based cohort, our aims were to 1) describe rhinitis, AR and NAR, and 2) explore how asthma and conjunctivitis may lead to the identification of novel rhinitis phenotypes. Methods In this cross-sectional analysis, current rhinitis was defined as present in the last 12 months using a questionnaire from the French CONSTANCES cohort. Participants with current rhinitis reporting nasal allergies were considered as AR, otherwise as NAR. We described AR and NAR phenotypes, and their phenotypes including co-occurrence with ever-asthma and ever-conjunctivitis. Results Among the 20 772 participants included in this analysis (mean± sd age 52.6±12.6 years; 55.2% female), crude prevalences of AR and NAR were 28.0% and 10.9%. AR participants more frequently reported persistent rhinitis (31.6% versus 25.1%) and moderate-to-severe rhinitis (40.1% versus 24.2%) than NAR participants. Among AR or NAR participants, those with ever-asthma reported more moderate-to-severe rhinitis. Participants with AR, ever-asthma and ever-conjunctivitis had an earlier age of rhinitis onset, more severe rhinitis and higher eosinophil counts than participants in other groups. Results were replicated in another cohort. Conclusions In this large population-based cohort, 40% reported current rhinitis, with a lower prevalence of moderate-to-severe rhinitis than in clinical practice. For the first time in a general adult population, we showed that AR and NAR alone or in combination with asthma or in combination with asthma and conjunctivitis are different phenotypes. These results provide new insights on how best to manage rhinitis and its multimorbidities.
Addressing Social Needs Through Medicare Advantage Plans’ Supplemental Benefits—A Potential Not Yet Realized
Authors: David J. Meyers, Emma Tucher, Kali S. Thomas
Journal: JAMA Network Open (2022)

Bonnie Jin, PhD, MPH; Lingshu Xue, PhD; John Lovelace, MS, MSIS; Donna Almario Doebler, DrPH, MS, MPH; Eric T. Roberts, PhD
Readmission Reduction as a Hospital Quality Measure
Authors: Peter Cram, Robert M. Wachter, Bruce E. Landon
Journal: JAMA (2022)

The authors of this Viewpoint argue that the focus on hospital readmission rates as a measure of quality during the past decade, although undoubtedly leading to some improvements in care, has had minimal demonstrable benefit and has even distracted clinicians and health system leaders from other crucial quality concerns.
U-BIOPRED/BIOAIR proteins: inflammation or infection?
Authors: David L. Hahn, Wilmore Webley
Journal: European Respiratory Journal (2022)

We would like to comment on the interesting report by Sparreman Mikus et al . [1] from the U-BIOPRED Group and the BIOAIR Consortium. The study identified 10 plasma proteins associated with severe asthma present in both the discovery (U-BIOPRED) and validation (BIOAIR) cohorts. These proteins included inflammatory cytokines, growth factors and chitinases, and also sphingolipid pathway, complement cascade and mast cell-related proteins. Notably, these associations were reported to be independent of steroid treatment, and unrelated to type-2 inflammation. We note that all these protein categories can be linked to pathogenesis of the infectious agents previously associated with asthma (rhinovirus, respiratory syncytial virus, adenovirus, Mycoplasma pneumoniae , Chlamydia pneumoniae and Chlamydia trachomatis ) [2–4]. The U-BIOPRED/BIOAIR proteins are associated with host responses to infections <https://bit.ly/3lO2S3r>
Reply: U-BIOPRED/BIOAIR proteins: inflammation or infection?
Authors: Maria Sparreman Mikus, Johan Kolmert, Lars I. Andersson, Sven-Erik Dahlén, Anna James
Journal: European Respiratory Journal (2022)

<b>Protein profiles in plasma remained associated with asthma severity in the European asthma cohort U-BIOPRED when controlling for previous history of respiratory infections</b>https://bit.ly/3rdEL0O
Broadening concepts of core pathobiology in various aspects of COPD development
Authors: Eugene H. Walters, Shakti Shukla, Chis Ward
Journal: European Respiratory Journal (2022)

<b>Linking the work of Xu and co-workers with the importance of small airway EMT and fibrosis/narrowing that leads to peri-bronchial air trapping and secondary emphysema: a core message in the understanding of COPD development needing more emphasis</b>https://bit.ly/3RsDT3K
Ventilation and tumour spread: still a pending matter
Authors: Liu Zhang, Fang Ying Lu, Shao Guang Huang, Qing Yun Li
Journal: European Respiratory Journal (2022)

The mechanism of ventilator-induced lung injury (VILI) has attracted considerable attention. López-Alonso et al . [1] reported that mechanical ventilation (MV) influenced lung tumour spread in European Respiratory Journal recently, which provides a novel perspective. For example, during respiratory failure or major surgery without removal of tumour, there might exist a potential risk of metastasis by MV for patients with lung tumours. The study verified that mechanical stretch regulated intracellular cholesterol through PCSK9, which in turn preserved cell stiffness and, subsequently, promoted lung tumour spread. In vivo , the mice were injected with melanoma cells via the jugular vein and were submitted to a 2-h period of MV (peak inspiratory pressure 15 cmH2O, positive end-expiratory pressure (PEEP) 2 cmH2O, 100 breaths per min) or spontaneous breathing, and the results showed that MV increased tumour invasiveness. In vitro , it was demonstrated that stretch increases invasiveness in melanoma B16F10luc2 and lung adenocarcinoma A549 cells. This work explored the effects of MV from a new point of view. However, there are several aspects that we feel need further discussion. López-Alonso and co-workers provided a novel perspective to the effects of mechanical ventilation on tumour spread, which needs further studies in the future <https://bit.ly/3xEa74l>
Surrogacy of Pathologic Complete Response in Trials of Neoadjuvant Therapy for Early Breast Cancer
Authors: Fabio Conforti, Laura Pala, Vincenzo Bagnardi, Tommaso De Pas, Marco Colleoni, Marc Buyse, Gabriel Hortobagyi, Luca Gianni, Eric Winer, Sibylle Loibl, Javier Cortes, Martine Piccart, Antonio C. Wolff, Giuseppe Viale, Richard D. Gelber
Journal: JAMA Oncology (2022)

The pathologic complete response (pCR) is supported by regulatory agencies as a surrogate end point for long-term patients' clinical outcomes in the accelerated approval process of new drugs tested in neoadjuvant randomized clinical trials (RCTs) for early breast cancer (BC). However, a meaningful association between pCR and patients' survival has been proven only at the patient level (ie, significantly better survival of patients who achieved pCR compared with those who did not), but not at trial level (ie, poor association between degree of improvement in pCR rate and survival reported across trials).We critically discuss the potential reasons of such discrepancy between pCR surrogacy value at the patient and trial level, as well as the relevant implications for both clinical research and drug regulatory policy. We also describe alternative surrogate end points, including combined end points that jointly analyzed pathological response and event-free survival data, or the assessment of circulating tumor DNA (ctDNA). Such proposed surrogate end points could overcome limits of pCR and provide a reasonable trade-off between the 2 conflicting needs to have access to effective therapies rapidly, and to reliably assess patients' clinical benefit.Using surrogate end points to grant drug approvals is justified only when they can provide accurate prediction of a drug's effect on the long-term patient outcomes. Evidence currently available does not support pCR used alone as a reliable surrogate end point in regulatory neoadjuvant RCTs for BC. The surrogacy value at trial level of potentially more robust surrogate end points needs to be urgently tested.
Is the Delphi’s Oracle Pertinent to Patients With Resectable and Borderline Resectable Pancreatic Ductal Adenocarcinoma?—Reply
Authors: J. Annelie Suurmeijer, Marc G. Besselink, Hanneke W. M. van Laarhoven
Journal: JAMA Oncology (2022)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA Oncology HomeNew OnlineCurrent IssueFor Authors Podcast Publications JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2023 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA Oncology journal
Examination of Differences in Nonmedical Supplemental Benefit Coverage for Dual-Eligible Enrollees in Medicare Advantage Plans in 2021
Authors: Bonnie Jin, Lingshu Xue, John Lovelace, Donna Almario Doebler, Eric T. Roberts
Journal: JAMA Network Open (2022)

This cross-sectional study uses Medicare Advantage benefit package data for 2021 to examine differences in the coverage of nonmedical supplemental benefits—such as transportation services and food and meal assistance—for dual-eligible enrollees with health-related social needs.
Is the Delphi’s Oracle Pertinent to Patients With Resectable and Borderline Resectable Pancreatic Ductal Adenocarcinoma?
Authors: Michele Reni, Marina Macchini, Giulia Orsi
Journal: JAMA Oncology (2022)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA Oncology HomeNew OnlineCurrent IssueFor Authors Podcast Publications JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2023 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA Oncology journal
A Large-Scale Prospective Concordance Study of Plasma- and Tissue-Based Next-Generation Targeted Sequencing for Advanced Non–Small Cell Lung Cancer (LC-SCRUM-Liquid)
Authors: Akira Sugimoto, Shingo Matsumoto, Hibiki Udagawa, Ryo Itotani, Yuko Usui, Shigeki Umemura, Kazumi Nishino, Ichiro Nakachi, Shoichi Kuyama, Haruko Daga, Satoshi Hara, Shingo Miyamoto, Terufumi Kato, Jun Sakakibara-Konishi, Eriko Tabata, Taku Nakagawa, Tomoya Kawaguchi, Tetsuya Sakai, Yuji Shibata, Hiroki Izumi, Kaname Nosaki, Yoshitaka Zenke, Kiyotaka Yoh, Koichi Goto
Journal: Clinical Cancer Research (2022)

We evaluated plasma cell-free DNA (cfDNA) and tissue-based sequencing concordance for comprehensive oncogenic driver detection in non-small cell lung cancer (NSCLC) using a large-scale prospective screening cohort (LC-SCRUM-Liquid).Blood samples were prospectively collected within 4 weeks of corresponding tumor tissue sampling from patients with advanced NSCLC to investigate plasma cfDNA sequencing concordance for alterations in 8 oncogenes (EGFR, KRAS, BRAF, HER2, MET, ALK, RET, and ROS1) compared with tissue-based next-generation targeted sequencing.Paired blood and tissue samples were obtained in 1,062/1,112 enrolled patients with NSCLC. Oncogenic alteration was detected by plasma cfDNA sequencing and tissue assay in 455 (42.8%) and 537 (50.5%) patients, respectively. The positive percent agreement of plasma cfDNA sequencing compared with tissue DNA and RNA assays were 77% (EGFR, 78%; KRAS, 75%; BRAF, 85%; HER2, 72%) and 47% (ALK, 46%; RET, 57%; ROS1, 18%; MET, 66%), respectively. Oncogenic drivers were positive for plasma cfDNA and negative for tissue due to unsuccessful genomic analysis from poor-quality tissue samples (70%), and were negative for plasma cfDNA and positive for tissue due to low sensitivity of cfDNA analysis (61%). In patients with positive oncogenic drivers by plasma cfDNA sequencing but negative by tissue assay, the response rate of genotype-matched therapy was 85% and median progression-free survival was 12.7 months.Plasma cfDNA sequencing in patients with advanced NSCLC showed relatively high sensitivity for detecting gene mutations but low sensitivity for gene fusions and MET exon 14 skipping. This may be an alternative only when tissue assay is unavailable due to insufficient DNA and RNA. See related commentary by Jacobsen Skanderup et al., p. 1381.
Respiratory Virus Surveillance Among Children with Acute Respiratory Illnesses — New Vaccine Surveillance Network, United States, 2016–2021
Authors: Ariana Perez, Joana Y. Lively, Aaron Curns, Geoffrey A. Weinberg, Natasha B. Halasa, Mary Allen Staat, Peter G. Szilagyi, Laura S. Stewart, Monica M. McNeal, Benjamin Clopper, Yingtao Zhou, Brett L. Whitaker, Elizabeth LeMasters, Elizabeth Harker, Janet A. Englund, Eileen J. Klein, Rangaraj Selvarangan, Christopher J. Harrison, Julie A. Boom, Leila C. Sahni, Marian G. Michaels, John V. Williams, Gayle E. Langley, Susan I. Gerber, Angela Campbell, Aron J. Hall, Brian Rha, Meredith McMorrow, Bonnie Strelitz, Kirsten Lacombe, Mary Moffatt, Jennifer Schuster, Chelsea Rohlfs, Miranda Howard, Yesenia Romero, James Chappell, Pedro A. Piedra, Vasanthi Avadhanula, Wende Fregoe, Christina Albertin, Robert H. Hickey, Judith M Martin
Journal: MMWR Morbidity and Mortality Weekly Report (2022)

The New Vaccine Surveillance Network (NVSN) is a prospective, active, population-based surveillance platform that enrolls children with acute respiratory illnesses (ARIs) at seven pediatric medical centers. ARIs are caused by respiratory viruses including influenza virus, respiratory syncytial virus (RSV), human metapneumovirus (HMPV), human parainfluenza viruses (HPIVs), and most recently SARS-CoV-2 (the virus that causes COVID-19), which result in morbidity among infants and young children (1-6). NVSN estimates the incidence of pathogen-specific pediatric ARIs and collects clinical data (e.g., underlying medical conditions and vaccination status) to assess risk factors for severe disease and calculate influenza and COVID-19 vaccine effectiveness. Current NVSN inpatient (i.e., hospital) surveillance began in 2015, expanded to emergency departments (EDs) in 2016, and to outpatient clinics in 2018. This report describes demographic characteristics of enrolled children who received care in these settings, and yearly circulation of influenza, RSV, HMPV, HPIV1-3, adenovirus, human rhinovirus and enterovirus (RV/EV),* and SARS-CoV-2 during December 2016-August 2021. Among 90,085 eligible infants, children, and adolescents (children) aged <18 years
Preliminary Incidence and Trends of Infections Caused by Pathogens Transmitted Commonly Through Food — Foodborne Diseases Active Surveillance Network, 10 U.S. Sites, 2016–2021
Authors: Jennifer P. Collins, Hazel J. Shah, Daniel Lowell Weller, Logan C. Ray, Kirk Smith, Suzanne McGuire, Rosalie T. Trevejo, Rachel H. Jervis, Duc J. Vugia, Tamara Rissman, Katie N. Garman, Sarah Lathrop, Bethany LaClair, Michelle M. Boyle, Stic Harris, Joanna Zablotsky Kufel, Robert V. Tauxe, Beau B. Bruce, Erica Billig Rose, Patricia M. Griffin, Daniel C. Payne
Journal: MMWR Morbidity and Mortality Weekly Report (2022)

To evaluate progress toward prevention of enteric infections in the United States, the Foodborne Diseases Active Surveillance Network (FoodNet) conducts active population-based surveillance for laboratory-diagnosed infections caused by Campylobacter, Cyclospora, Listeria, Salmonella, Shiga toxin-producing Escherichia coli (STEC), Shigella, Vibrio, and Yersinia at 10 U.S. sites. This report summarizes preliminary 2021 data and describes changes in annual incidence compared with the average annual incidence for 2016-2018, the reference period for the U.S. Department of Health and Human Services' (HHS) Healthy People 2030 goals for some pathogens (1). During 2021, the incidence of infections caused by Salmonella decreased, incidence of infections caused by Cyclospora, Yersinia, and Vibrio increased, and incidence of infections caused by other pathogens did not change. As in 2020, behavioral modifications and public health interventions implemented to control the COVID-19 pandemic might have decreased transmission of enteric infections (2). Other factors (e.g., increased use of telemedicine and continued increase in use of culture-independent diagnostic tests [CIDTs]) might have altered their detection or reporting (2). Much work remains to achieve HHS Healthy People 2030 goals, particularly for Salmonella infections, which are frequently attributed to poultry products and produce, and Campylobacter infections, which are frequently attributed to chicken products (3).